title: MPRA from K562 (ENCLB892DQK)

description:
https://www.encodeproject.org/experiments/ENCSR753ZRI/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR753ZRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB892DQK
fragmentation methods: none

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

value: adult

value: 53 years

tag: passage number

tag: source

value: ENCBS519XFS at ENCODE; https://www.encodeproject.org/ENCBS519XFS/


title: MSLN-CAR T-CM, replicate 3

status: Public on May 07 2024

type: SRA

city: PHILADELPHIA

first: Wei

last: Guo

state: PENNSYLVANIA

address: 433 S. University Avenue

country: USA

institute: University of Pennsylvania

description:
MSLN-CAR T-CM, replicate 3
A15

library_source: transcriptomic

data_processing:
platforms, according to effective library concentration and data amount.
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean2 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tool
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression
Assembly: mm10
Supplementary files format and content: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.

molecule: total RNA

organism: Mus musculus

growth_protocol: Mouse Meso-CAR was constructed by fusing anti-mesothelin scFv to a mouse CD3-ζ signaling domain and a mouse 4-1BB co-stimulatory domain along with a EGFP tag. The CAR was subcloned into the MSGV vector and packaged in the Phoenix packaging cells (Allele; Phoenix Eco Cells Line ABP-RVC-10002; purchased from and authenticated by ATCC, CRL-3214, RRID: CVCL_H717) to obtain the retrovirus. T cells were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin sulfate, 1 mM pyruvate and 50 μM β-mercaptoethanol. Primary mouse T cells were isolated as suggested by the manufacturer (Miltenyi Biotec) from the spleens of mice and incubated in 12-well plates (2 × 106 cells per well), and Dynabeads Mouse T-Activator CD3/CD28 (Gibco, Cat#: 11453D) at a 1:1 ratio

extract_protocol:
cells were collected and total RNA was extracted using an invitrogen PureLink RNA Mini Kit.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for
size distribution detection. Quantified libraries will be pooled and sequenced on Illumina

tag: cell line

tag: cell type

value: mouse T cells

tag: genotype

value: WT

tag: treatment

value: MSLN-CAR T-CM


title: S1 cortex, Csf1r KO, poly(I:C), replicate 1

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: snRNA-seq

molecule: nuclear RNA

source_name: S1 cortex

extract_protocol:
For single-cell microglia isolates: Somatosensory (S1) cortex was dissected and meninges removed. S1 cortex blocks were minced and pelleted at 500g for 5 minutes. The pellet was resuspended in 1mL dissociation buffer (20mL PBS + 20uL RNasin + 400uL DNAse). The tissue was homogenized with 15 plunges of pestle "A" and passed through a 70um cell strainer, and pelleted at 500g for 5 minutes. The pellet was resuspended in 500uL FACS buffer (PBS with 0.04% BSA). Cells were labelled with anti-Cd11b-PE, anti-Cx3cr1-APC, and anti-Cd45-APC/Cy7, and FACS sorted to isolate microglia. For single-nucleus S1 cortex samples from Csf1r null and WT mice: Prospective S1 cortices of E15.5 embryos were dissected and flash-frozen in liquid nitrogen and stored at -80C. Frozen tissue blocks from male Csf1r mutant and WT embryos were processed to obtain a single-cell suspension using papain digestion (15 minutes) (Papain dissociation kit, Worthington), following the manufacturer’s protocol. After dissociation and concentration, the pellet was resuspended in 500 uL of Nuclei Solubilization Buffer (10 mL PBS (Gibco, 15630-080) + 50 uL of 20 mg/mL BSA (NEB, B9000S) + 10 uL RNasin (Promega, N26515)) spiked with 1 uL of Hoechst and passed through a 40 um filter (Corning 352235). Nuclei were sorted on a Beckman Coulter MoFlo Astrios EQ Cell Sorter, pre-chilled to 4C, using a 100 um nozzle, and collected into wells of a 96-well plate pre-filled with 10 uL of Nuclei Solubilization Buffer, and immediately processed for single-cell GEM formation (10x Genomics, single cell RNA sequencing 3’, Chromium v3.1).
Libraries were prepared according to manufacturer's insctructions using Chromium Single Cell 3' Kit v3.1 (10X Genomics, PN-1000121).

treatment_protocol: Mothers were given intraperitoneal injections at E12.5 of either poly(I:C) to induce maternal immune activation, or saline as a control.

tag: tissue

value: S1 cortex

tag: Sex

value: Male

tag: developmental stage

tag: strain


title: MSLN-CAR T-CM, replicate 2

description:
MSLN-CAR T-CM, replicate 2
A13


title: S1 cortex, WT, nacl, replicate 2

description: 10X Genomics

value: saline


title: MPRA from K562 (ENCLB798KQF)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR753ZRI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR753ZRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB798KQF
fragmentation methods: none

data_processing: See GSM*_README.txt supplementary file linked below

organism: Homo sapiens

tag: line

value: cell line

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

tag: health state

tag: age

tag: lab

value: Ryan Tewhey, JAX

value: ATCC

tag: link

value: ENCBS570HQL at ENCODE; https://www.encodeproject.org/ENCBS570HQL/


title: S1 cortex, Csf1r KO, nacl, replicate 1

description: 10X Genomics


title: MSLN-CAR T-CM, replicate 1

description:
MSLN-CAR T-CM, replicate 1
A11

tag: cell line


title: E12, microglia, developing cortex, replicate 2

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 and v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Developing microglia atlas samples were further processed with the Kallisto | Bustools pipeline (https://www.kallistobus.tools/)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For single-cell microglia isolates: Somatosensory (S1) cortex was dissected and meninges removed. S1 cortex blocks were minced and pelleted at 500g for 5 minutes. The pellet was resuspended in 1mL dissociation buffer (20mL PBS + 20uL RNasin + 400uL DNAse). The tissue was homogenized with 15 plunges of pestle "A" and passed through a 70um cell strainer, and pelleted at 500g for 5 minutes. The pellet was resuspended in 500uL FACS buffer (PBS with 0.04% BSA). Cells were labelled with anti-Cd11b-PE, anti-Cx3cr1-APC, and anti-Cd45-APC/Cy7, and FACS sorted to isolate microglia.
Libraries were prepared according to manufacturer's insctructions using Chromium Single Cell 3' Kit v3.1 (10X Genomics, PN-1000121).

tag: cell type

value: microglia

value: Mixed


title: MPRA from K562 (ENCLB191IIV)

description:
https://www.encodeproject.org/experiments/ENCSR753ZRI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR753ZRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB191IIV
fragmentation methods: none

value: female

value: chronic myelogenous leukemia (CML)

tag: dev stage

tag: passage number

tag: source

value: ENCBS149ALX at ENCODE; https://www.encodeproject.org/ENCBS149ALX/


title: S1 cortex, WT, poly(I:C), replicate 1

description: 10X Genomics

tag: tissue

tag: Sex

tag: genotype

tag: treatment


title: UTD-CM, replicate 1

description:
UTD-CM, replicate 1
A10

value: UTD-CM


title: MPRA from K562 (ENCLB887JPA)

description:
https://www.encodeproject.org/experiments/ENCSR753ZRI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR753ZRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB887JPA
fragmentation methods: none

tag: line

tag: biosample encode accession

value: adult

value: 53 years

value: ENCBS297VWO at ENCODE; https://www.encodeproject.org/ENCBS297VWO/


title: S1 cortex, WT, nacl, replicate 1

description: 10X Genomics

value: S1 cortex

tag: developmental stage

tag: strain

value: WT


title: NT_rep3

city: Manchester

first: Simon

last: Williams

address: Oxford Road

country: United Kingdom

institute: The University of Manchester

description: Libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422

data_processing:
Output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422
Pseudo-alignment and subsequent transcript expression values were determined using Kallisto (v 0.43.0)
Assembly: GRCh38 ensembl rel103 transcriptome
Supplementary files format and content: tab-delimited text files including TPM values for transcripts in each sample

source_name: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)

extract_protocol:
RNA was harvested using the RNeasy Plus Kit (Qiagen) following manufacturer’s instructions. 1 μg of total RNA/sample was used for the generation of sequencing libraries
Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library.

value: WT (no transfection)


title: MPRA from K562 (ENCLB376XTE)

description:
https://www.encodeproject.org/experiments/ENCSR753ZRI/
***************
biological replicate number: 6
technical replicate number: 1
description:
experiment encode accession: ENCSR753ZRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB376XTE
fragmentation methods: none

value: cell line

tag: collection date

tag: geographic location

tag: encode accession

tag: health state

value: ENCBS112TUD at ENCODE; https://www.encodeproject.org/ENCBS112TUD/


title: P14, microglia, MIA, replicate 2

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: UTD-CM, replicate 3

description:
UTD-CM, replicate 3
A14

tag: cell line

value: mouse T cells


title: NT_rep2

tag: cell type

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)


title: EV_rep3

value: WT (empty vector)


title: P14, microglia, MIA, replicate 1

description: 10X Genomics

value: microglia


title: MPRA from SK-N-SH (ENCLB036ZYT)

description:
https://www.encodeproject.org/experiments/ENCSR541FWB/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR541FWB
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB036ZYT
fragmentation methods: none

source_name: Homo sapiens SK-N-SH cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

value: SK-N-SH

value: not applicable

value: Metastatic neuroblastoma from bone marrow

tag: dev stage

value: child

tag: age

value: 4 years

tag: lab

value: Ryan Tewhey, JAX

value: ATCC

tag: link

value: ENCBS554AQV at ENCODE; https://www.encodeproject.org/ENCBS554AQV/


title: MPRA from SK-N-SH (ENCLB873LVF)

description:
https://www.encodeproject.org/experiments/ENCSR541FWB/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR541FWB
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB873LVF
fragmentation methods: none

tag: Sex

value: female

tag: passage number

tag: source

value: ENCBS549WKB at ENCODE; https://www.encodeproject.org/ENCBS549WKB/


title: P14, microglia, nacl, replicate 3, male

description: 10X Genomics

tag: tissue

value: S1 cortex

value: Male

tag: genotype

value: WT

tag: treatment

value: saline


title: EV_rep1

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)


title: MPRA from K562 (ENCLB829MNT)

description:
https://www.encodeproject.org/experiments/ENCSR753ZRI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR753ZRI
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB829MNT
fragmentation methods: none

tag: line

value: cell line

tag: biosample encode accession

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: ENCBS085IOP at ENCODE; https://www.encodeproject.org/ENCBS085IOP/


title: MPRA from SK-N-SH (ENCLB045UNE)

description:
https://www.encodeproject.org/experiments/ENCSR541FWB/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR541FWB
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB045UNE
fragmentation methods: none

value: SK-N-SH

tag: collection date

value: not applicable

tag: geographic location

value: Metastatic neuroblastoma from bone marrow

value: child

value: ENCBS915MUF at ENCODE; https://www.encodeproject.org/ENCBS915MUF/


title: UTD-CM, replicate 2

description:
UTD-CM, replicate 2
A12

value: mouse T cells

value: UTD-CM


title: P14, microglia, nacl, replicate 3, female

description: 10X Genomics

value: microglia

value: S1 cortex

value: Female

tag: developmental stage

tag: strain


title: P14, microglia, nacl, replicate 2

description: 10X Genomics

tag: cell type

value: Mixed

value: WT

value: saline


title: NT_rep1

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)

value: WT (no transfection)


title: MPRA from SK-N-SH (ENCLB985KXH)

description:
https://www.encodeproject.org/experiments/ENCSR541FWB/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR541FWB
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB985KXH
fragmentation methods: none

value: cell line

tag: encode accession

value: female

tag: health state

tag: dev stage

value: 4 years

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS423WOQ at ENCODE; https://www.encodeproject.org/ENCBS423WOQ/


title: EV_rep2

value: WT (empty vector)


title: FLT4_TOF-PTV_rep3


title: P14, microglia, nacl, replicate 1

description: 10X Genomics


title: FLT4_TOF-PTV_rep2


title: E15, microglia, MIA, replicate 3

description: 10X Genomics


title: MPRA from HepG2 (ENCLB002SYG)

description:
https://www.encodeproject.org/experiments/ENCSR463DWN/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR463DWN
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB002SYG
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: not applicable

value: male

value: hepatocellular carcinoma

value: child

tag: age

value: 15 years

tag: lab

tag: link

value: ENCBS091CXO at ENCODE; https://www.encodeproject.org/ENCBS091CXO/


title: E15, microglia, MIA, replicate 2

description: 10X Genomics

value: microglia

value: S1 cortex

tag: Sex

value: Mixed

value: WT


title: MPRA from HepG2 (ENCLB637DPX)

description:
https://www.encodeproject.org/experiments/ENCSR463DWN/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR463DWN
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB637DPX
fragmentation methods: none

value: cell line

tag: passage number

tag: source

value: ENCBS589IFU at ENCODE; https://www.encodeproject.org/ENCBS589IFU/


title: FLT4_TOF-PTV_rep1

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)

tag: genotype


title: MPRA from SK-N-SH (ENCLB867YSB)

description:
https://www.encodeproject.org/experiments/ENCSR541FWB/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR541FWB
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB867YSB
fragmentation methods: none

tag: line

value: SK-N-SH

value: female

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: Ryan Tewhey, JAX

value: ENCBS435OUB at ENCODE; https://www.encodeproject.org/ENCBS435OUB/


title: E15, microglia, MIA, replicate 1

description: 10X Genomics

tag: tissue

tag: treatment


title: MPRA from HepG2 (ENCLB498TJE)

description:
https://www.encodeproject.org/experiments/ENCSR447RLV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR447RLV
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB498TJE
fragmentation methods: none

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

value: male

value: hepatocellular carcinoma

value: ATCC

value: ENCBS876UOK at ENCODE; https://www.encodeproject.org/ENCBS876UOK/


title: FLT4_TOF-DNV_rep3

tag: cell type


title: MPRA from HepG2 (ENCLB989SLT)

description:
https://www.encodeproject.org/experiments/ENCSR447RLV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR447RLV
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB989SLT
fragmentation methods: none

tag: encode accession

value: child

value: 15 years

value: ENCBS020JFP at ENCODE; https://www.encodeproject.org/ENCBS020JFP/


title: MPRA from K562 (ENCLB573BSY)

description:
https://www.encodeproject.org/experiments/ENCSR394HXI/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR394HXI
assay title: MPRA
assembly: hg19
possible controls: ENCSR367WAO
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB573BSY
fragmentation methods: none

source_name: Homo sapiens K562 cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

value: cell line

tag: health state

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: ENCBS984RTL at ENCODE; https://www.encodeproject.org/ENCBS984RTL/


title: FLT4_TOF-DNV_rep1

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)


title: MPRA from K562 (ENCLB841HTB)

description:
https://www.encodeproject.org/experiments/ENCSR394HXI/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR394HXI
assay title: MPRA
assembly: hg19
possible controls: ENCSR367WAO
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB841HTB
fragmentation methods: none

value: female

tag: dev stage

value: ENCBS886BLC at ENCODE; https://www.encodeproject.org/ENCBS886BLC/


title: FLT4_MD_rep3


title: E13, microglia, MIA, replicate 3

description: 10X Genomics

value: microglia

value: S1 cortex

value: Mixed

tag: developmental stage

tag: strain

value: WT


title: FLT4_TOF-DNV_rep2


title: FLT4_MD_rep2


title: MPRA from K562 (ENCLB571GOB)

description:
https://www.encodeproject.org/experiments/ENCSR394HXI/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR394HXI
assay title: MPRA
assembly: hg19
possible controls: ENCSR367WAO
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB571GOB
fragmentation methods: none

value: not applicable

tag: age

tag: lab

value: Ryan Tewhey, JAX

value: ATCC

tag: link

value: ENCBS073BZW at ENCODE; https://www.encodeproject.org/ENCBS073BZW/


title: MPRA from K562 (ENCLB199QXL)

description:
https://www.encodeproject.org/experiments/ENCSR394HXI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR394HXI
assay title: MPRA
assembly: hg19
possible controls: ENCSR367WAO
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB199QXL
fragmentation methods: none

tag: Sex

tag: passage number

tag: source

value: ENCBS984HVY at ENCODE; https://www.encodeproject.org/ENCBS984HVY/


title: MPRA from HepG2 (ENCLB309PMS)

description:
https://www.encodeproject.org/experiments/ENCSR354FXV/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR354FXV
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB309PMS
fragmentation methods: none

source_name: Homo sapiens HepG2 cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

tag: line

value: cell line

value: male

value: hepatocellular carcinoma

value: child

value: 15 years

value: ENCBS033NBO at ENCODE; https://www.encodeproject.org/ENCBS033NBO/


title: MNase-ChIP, Input, Ash1 RNAi, Batch 7

city: Munich

first: Muhunden

middle: Nallappa

last: Jayakrishnan

state: Munich (city)

address: 57 Nusselstrasse, 57

department: Molecular Biology

country: Germany

institute: Biomedical Center, Ludwig Maximilians University Munich

library_source: genomic

data_processing:
MNase-based paired-end ChIP-seq reads were demultiplexed using JEDemultiplexer and concordantly aligned using Bowtie2 with -X 500 and were filtered using samtools with parameter -q 10. Tag directories and coverage files (normalized to total number of virilis reads and to input) were generated by Homer Software package (Heinz et al. 2010).
Peak calling was performed on replicate-averaged normalized coverages using MACS2 v2.1.2 bdgpeakcall with parameters -l 1000 -c 3
Regions of differential K36me1/2/3 binding upon RNAi were identified using csaw v1.24.3 using BAM files obtained from bowtie2 for all replicates as input. 250bp windows of signficant difference were merged into regions of max 3kb.
Assembly: BDGP6 (dm6), release 104
Supplementary files format and content: For ChIPs, D. virilis scaled and input normalized .bigwig are provided for each individual sample. For inputs, representative D.virilis scaled .bigwig are provided.
Supplementary files format and content: Control K36me1/2/3 peaks as .bed (provided as supplementary to Control RNAi ChIP files)
Supplementary files format and content: csaw output of regions of significant change as .bed (provided as supplementary to HMT RNAi ChIP files except Batch0)

molecule: genomic DNA

organism: Drosophila melanogaster

growth_protocol: Cells were cultured in Schneider’s Drosophila Medium (Thermo Fisher), supplemented with 10% heat-inactivated Fetal Bovine Serum (Sigma‑Aldrich), 100 units/mL penicillin and 0.1mg/mL streptomycin (Sigma‑Aldrich).

extract_protocol:
70 to 130 million RNAi treated S2 cells, resuspended in 20 ml of complete Schneider’s Drosophila Medium, were crosslinked by adding 1:10 of the volume of Fixing Solution (100 mM NaCl, 50 mM Hepes pH 8, 1mM EDTA, 0.5 mM EGTA, 10% methanol-free formaldehyde) and rotated at room temperature for 8 min. 1.17 ml of freshly-prepared 2.5 M glycine was added to stop the fixation (final conc. 125 mM). Cells were pelleted at 500 g for 10 min (4°C) and resuspended in 10 mL of ice-cold PBS. 3.5 million of fixed D. virilis cells (fixed as described for D. melanogaster cells) were added for every 70 million D. melanogaster cells. Cells were pelleted at 526 g for 10 min (4°C) and resuspended in 1 ml of PBS + 0.5% Triton-X-100 + 1X cOmplete EDTA-free Protease Inhibitor for every 70 million D. melanogaster cells and rotated at 4°C for 15 min to release nuclei. Nuclei were pelleted at 2000 g for 10 min and washed once with 10 ml of ice-cold PBS. Nuclei were suspended in 1 ml of RIPA buffer (10 mM Tris-HCl pH 8, 140 mM NaCl, 1mM EDTA, 0.1% Na-deoxycholate, 1% Triton-X-100, 0.1% SDS, 1 mM PMSF, 1X cOmplete EDTA-free Protease Inhibitor + Roche 1x PhosSTOP) + 2 mM CaCl2 for every 70 million D. melanogaster cells, divided into 1 ml aliquots and flash-frozen in liquid N2. 1 mL of fixed nuclei was quickly thawed and 1 µL of MNase (to 0.6 units) (Sigma-Aldrich, Cat. No N5386) added. Chromatin was digested for 35 min at 37°C. MNase digestion was stopped by transferring the samples on ice and adding 22 µL of 0.5 M EGTA. Samples were mildly sonicated using a Covaris S220 instrument with the following settings: 50 W peak power, 20% duty factor, 200 cycles/burst, 8 min total time. Insoluble chromatin was removed by centrifugation at 16,000 g for 30 min at 4°C. Soluble chromatin was pre-cleared by incubation with 10 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry (GE Healthcare, Cat. No 17-5280-11 and 17-0618-06) for every 100 µL of chromatin for 1 h at 4°C. 100 µL of pre-cleared chromatin were set aside (input) and kept overnight at 4°C, while each primary antibody was added to 300 µL of chromatin and incubated overnight at 4°C. 40 µL of 50% RIPA-equilibrated Protein A + G sepharose bead slurry was added for each immunoprecipitation and rotated 3 h at 4°C. Beads were washed 5 times with 1 ml of RIPA (5 min rotation at 4°C, pelleted at 3000 g for 1 min between washes) and resuspended in 100 µL of TE (10 mM Tris pH 8, 1 mM EDTA). 0.5 µL of RNaseA (Sigma-Aldrich, Cat. No. R4875) was added to both input samples and resuspended beads, followed by incubation at 37°C for 30 min. After addition of 6 µL of 10% SDS, protease digestion (250 ng/ µL Proteinase K, Genaxxon, Cat.no. M3036.0100) and crosslink reversal were performed simultaneously at 68°C for 2 hr. DNA was purified using 1.8X Agencourt AMPure XP beads (Beckman Coulter, Cat No A63880) following the standard protocol and eluted in 30 µL of 5 mM Tris-HCl pH 8. Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465). Libraries were sequenced on an Illumina NextSeq 1000 instrument at the Laboratory of Functional Genomic Analysis (LAFUGA, Gene Center Munich, LMU).
Standard Paired-end protocol using 5-10ng input material using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465).  Dual index oligos from NEB (#E6440). Libraries were size selected in 200-500 bp range and validated using Agilent TapeStation system.

treatment_protocol: RNAi against target genes in S2 cells was performed as previously described (Albig et al., 2016) with minor modifications. In brief, double-stranded RNA fragments (dsRNA) were generated with HiScribe T7 kit (NEB) from PCR products. Cells were incubated with 10 µg dsRNA per 1x10e6 cells (2 distinct sequences per target) in either 6 well plates or 75 cm^2 flasks for 1 hour. Two volumes of growth medium were added and cells were incubated at 26°C. Depending on the experiment, total duration of RNAi was 7-12 days with 2-3 rounds of fresh RNAi treatments.

tag: cell line

value: Late-stage Embryonic

tag: treatment

value: Ash1 RNAi


title: MNase-ChIP, Input, DKD (Set2+NSD) RNAi, Batch 5

value: Set2+NSD RNAi


title: MNase-ChIP, Input, DKD (Set2+NSD) RNAi, Batch 2


title: E13, microglia, MIA, replicate 2

description: 10X Genomics

value: microglia

tag: tissue

value: S1 cortex

tag: genotype


title: FLT4_MD_rep1

description: Libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422

tag: cell type

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)


title: E13, microglia, nacl, replicate 3

description: 10X Genomics

value: Mixed

value: WT

value: saline


title: FLT4_WT_rep3


title: FLT4_WT_rep2


title: MNase-ChIP, Input, NSD RNAi, Batch 7

value: NSD RNAi


title: E15, microglia, nacl, replicate 2

description: 10X Genomics


title: MPRA from HepG2 (ENCLB036MGP)

description:
https://www.encodeproject.org/experiments/ENCSR354FXV/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR354FXV
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB036MGP
fragmentation methods: none

tag: biosample encode accession

tag: collection date

value: not applicable

tag: geographic location

tag: encode accession

value: Ryan Tewhey, JAX

value: ATCC

value: ENCBS783QXE at ENCODE; https://www.encodeproject.org/ENCBS783QXE/


title: MPRA from HepG2 (ENCLB738NVF)

description:
https://www.encodeproject.org/experiments/ENCSR354FXV/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR354FXV
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB738NVF
fragmentation methods: none

value: cell line

value: male

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

value: ENCBS947ABS at ENCODE; https://www.encodeproject.org/ENCBS947ABS/


title: E13, microglia, nacl, replicate 2

description: 10X Genomics

tag: developmental stage

tag: strain


title: E15, microglia, nacl, replicate 3

description: 10X Genomics

tag: Sex


title: MNase-ChIP, Input, NSD RNAi, Batch 5

value: Late-stage Embryonic


title: MPRA from HepG2 (ENCLB508NHA)

description:
https://www.encodeproject.org/experiments/ENCSR354FXV/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR354FXV
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB508NHA
fragmentation methods: none

tag: age

value: 15 years

tag: passage number

tag: lab

tag: link

value: ENCBS887IOB at ENCODE; https://www.encodeproject.org/ENCBS887IOB/


title: E13, microglia, nacl, replicate 1

description: 10X Genomics

value: microglia

value: S1 cortex

tag: treatment


title: FLT4_WT_rep1

value: primary human umbilical vein endothelial cells, undifferentiated (passage 4 or less)


title: T1D_Patient_8_RNA_RNAseq_2

city: Boston

first: Eiichiro

last: Satake

address: One Joslin Place

department: Genetics and Epidemiology

institute: Joslin Diabetes Center

data_processing:
For edgeSeq, the sequencing data were imported into HTG EdgeSeq Parser software to align the FASTQ files obtained from the sequencer to miRBase v.21 sequences.
For RNASeq_1, data were analyzed using a SeqMatic in-house pipeline that included initial processing and demultiplexing using Illumina’s CASAVA v1.8.2 software pipeline
For RNASeq_2, small RNA sequencing data were analyzed using ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, low complexity, common RNA families and repeats. Unique sequences with length in 18-26 nucleotide were then mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Assembly: miRBase v21
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include normalized CPM counts for each platform

source_name: plasma

extract_protocol:
For the edgeSeq and RNASeq_1, total RNA was isolated from the selected samples using 180 µl of plasma from each individual and Qiagen’s miRNeasy Serum/Plasma kit (QIAGEN, Valencia, CA) according to the manufacturer’s protocol as previously published.
For small RNASeq performed by RNASeq_2, total RNA was extracted by the company from 200 ml of plasma using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure.
For the edgeSeq, the library was prepared using HTG EdgeSeq PCR processing and quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing.
For RNASeq_1, SeqMatic’s TailorMix miRNA Sample Preparation Kit V2 was used according to the manufacturer’s recommendations
For RNASeq_2, total RNA was used to prepare small RNA libraries using the commercially available TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, USA) according to the manufacturer’s protocol.

tag: tissue

value: plasma


title: MNase-ChIP, Input, NSD RNAi, Batch 2

tag: cell line

value: NSD RNAi


title: E15, microglia, nacl, replicate 1

description: 10X Genomics

tag: cell type

value: Mixed

tag: genotype

value: WT

value: saline


title: MPRA from K562 (ENCLB316VPU)

description:
https://www.encodeproject.org/experiments/ENCSR326HQU/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR326HQU
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB316VPU
fragmentation methods: none

tag: line

tag: biosample encode accession

tag: collection date

value: not applicable

value: female

value: chronic myelogenous leukemia (CML)

value: adult

value: 53 years

value: Ryan Tewhey, JAX

tag: source

value: ATCC

value: ENCBS511ILY at ENCODE; https://www.encodeproject.org/ENCBS511ILY/


title: T1D_Patient_7_RNA_RNAseq_2


title: E13, microglia, MIA, replicate 1

description: 10X Genomics


title: Jun-2day-2_CUTTag

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

country: China

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
The CUT&Tag reads were aligned to the mm10 genome by using Bowtie2. Low-mapping-quality reads were filtered by SAMtools (v.1.9), and duplicate reads were removed by Picard tools (v1.90).MACS2 (41) was used to call，peaks with a q-value < 0.01. BigWig files were generated by deeptools (46) by theRPKM normalization method and visualized in igv (v.2.13.1)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: bone-marrow-derived macrophage

extract_protocol:
Genomic DNA was extracted after tagementation of Tn5 transposome. Barcoded libraries were then amplified with PCR reactions (TruePrep DNA Library Prep Kit V2 for Illumina, Vazyme)
CUT&Tag libraries were constructed with CUT&Tag Assay Kit (pAG-Tn5) for illumina, (Abclonal)

value: bone-marrow-derived macrophage

value: Osteoclastic differentiation

tag: time

tag: antibody

value: Jun


title: Jun-2day-1_CUTTag


title: T1D_Patient_6_RNA_RNAseq_2


title: MNase-ChIP, Input, Set2 RNAi, Batch 7

value: Late-stage Embryonic

value: Set2 RNAi


title: MPRA from K562 (ENCLB825LQW)

description:
https://www.encodeproject.org/experiments/ENCSR326HQU/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR326HQU
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB825LQW
fragmentation methods: none

value: cell line

tag: geographic location

tag: encode accession

tag: health state

tag: dev stage

value: ENCBS662GKY at ENCODE; https://www.encodeproject.org/ENCBS662GKY/


title: Jun-0day-2_CUTTag

value: WT


title: MPRA from K562 (ENCLB542XVB)

description:
https://www.encodeproject.org/experiments/ENCSR326HQU/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR326HQU
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB542XVB
fragmentation methods: none

tag: Sex

tag: age

tag: passage number

tag: lab

value: ENCBS636EHL at ENCODE; https://www.encodeproject.org/ENCBS636EHL/


title: MNase-ChIP, Input, Set2 RNAi, Batch 5

tag: cell line

tag: treatment


title: T1D_Patient_4_RNA_RNAseq_2

tag: tissue

value: plasma


title: MPRA from K562 (ENCLB797UEA)

description:
https://www.encodeproject.org/experiments/ENCSR326HQU/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR326HQU
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB797UEA
fragmentation methods: none

tag: line

value: not applicable

value: female

tag: link

value: ENCBS156VTU at ENCODE; https://www.encodeproject.org/ENCBS156VTU/


title: MPRA from Jurkat (ENCLB669BZB)

description:
https://www.encodeproject.org/experiments/ENCSR247RPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR247RPW
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB669BZB
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

source_name: Homo sapiens Jurkat cell line genetically modified (episome) using transient transfection, 48 hours post-nucleic acid delivery time

value: Jurkat

tag: biosample encode accession

tag: collection date

value: male

value: acute T cell leukemia

value: child

value: 14 years

value: ENCBS390SXN at ENCODE; https://www.encodeproject.org/ENCBS390SXN/


title: MNase-ChIP, Input, Set2 RNAi, Batch 2

tag: cell type


title: fos-2day-2_CUTTag

value: bone-marrow-derived macrophage

tag: genotype

value: Osteoclastic differentiation

tag: time

tag: antibody

value: Fos


title: T1D_Patient_3_RNA_RNAseq_2


title: T1D_Patient_5_RNA_RNAseq_2


title: MNase-ChIP, Input, Set2 RNAi, Batch 1

value: Late-stage Embryonic

value: Set2 RNAi


title: fos-2day-1_CUTTag

value: WT


title: MNase-ChIP, Input, Control_2 RNAi, Batch 7

value: Control RNAi


title: MPRA from Jurkat (ENCLB388PKL)

description:
https://www.encodeproject.org/experiments/ENCSR247RPW/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR247RPW
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB388PKL
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

value: cell line

tag: geographic location

tag: encode accession

tag: health state

value: Ryan Tewhey, JAX

tag: source

value: ATCC

value: ENCBS656DXC at ENCODE; https://www.encodeproject.org/ENCBS656DXC/


title: fos-0day-2_CUTTag


title: T1D_Patient_1_RNA_RNAseq_2

value: plasma


title: T1D_Patient_2_RNA_RNAseq_2


title: MPRA from Jurkat (ENCLB127OCN)

description:
https://www.encodeproject.org/experiments/ENCSR247RPW/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR247RPW
assay title: MPRA
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB127OCN
fragmentation methods: none
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

value: Jurkat

value: not applicable

tag: Sex

value: male

tag: dev stage

tag: age

tag: passage number

value: ENCBS526QUG at ENCODE; https://www.encodeproject.org/ENCBS526QUG/


title: MNase-ChIP, Input, Control_2 RNAi, Batch 6

tag: cell line

tag: treatment


title: fos-0day-1_CUTTag


title: pooled clone sequencing from DNA cloning sample (ENCLB681MHD)

description:
https://www.encodeproject.org/experiments/ENCSR992PQH/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR992PQH
assay title: pooled clone sequencing
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB681MHD

organism: synthetic construct

source_name: control

value: DNA cloning sample

value: cloning host

tag: biosample term name

value: synthetic construct

value: 60 days

tag: lab


title: MPRA from HepG2 (ENCLB689MNT)

description:
https://www.encodeproject.org/experiments/ENCSR222QJT/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR222QJT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB689MNT
fragmentation methods: none

tag: line

tag: biosample encode accession

tag: collection date

value: hepatocellular carcinoma

value: child

value: 15 years

tag: link

value: ENCBS836YLI at ENCODE; https://www.encodeproject.org/ENCBS836YLI/


title: MNase-ChIP, Input, Control RNAi, Batch 5

tag: cell type

value: Late-stage Embryonic

value: Control RNAi


title: Jun-0day-1_CUTTag

value: bone-marrow-derived macrophage

tag: genotype

value: WT

value: Osteoclastic differentiation

tag: time

tag: antibody

value: Jun


title: MPRA from HepG2 (ENCLB405GFW)

description:
https://www.encodeproject.org/experiments/ENCSR222QJT/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR222QJT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB405GFW
fragmentation methods: none

value: cell line

value: not applicable

tag: geographic location

tag: encode accession

tag: health state

value: Ryan Tewhey, JAX

tag: source

value: ATCC

value: ENCBS361PJK at ENCODE; https://www.encodeproject.org/ENCBS361PJK/


title: pooled clone sequencing from DNA cloning sample (ENCLB858BCC)

description:
https://www.encodeproject.org/experiments/ENCSR732JTP/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR732JTP
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB858BCC

value: DNA cloning sample

value: cloning host

value: synthetic construct

tag: age

tag: Sex


title: ctrl_CUTTag

tag: treatment

value: ctrl


title: MNase-ChIP, Input, Control RNAi, Batch 4

tag: cell line


title: MPRA from HepG2 (ENCLB206FND)

description:
https://www.encodeproject.org/experiments/ENCSR222QJT/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR222QJT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB206FND
fragmentation methods: none

value: male

value: hepatocellular carcinoma

tag: dev stage

value: child

value: 15 years

tag: passage number

tag: lab

value: ENCBS630DUD at ENCODE; https://www.encodeproject.org/ENCBS630DUD/


title: pooled clone sequencing from DNA cloning sample (ENCLB061HEO)

description:
https://www.encodeproject.org/experiments/ENCSR732JTP/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR732JTP
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB061HEO

tag: biosample encode accession

tag: biosample term name

value: 60 days


title: pooled clone sequencing from DNA cloning sample (ENCLB969VKD)

description:
https://www.encodeproject.org/experiments/ENCSR732JTP/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR732JTP
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB969VKD


title: MPRA from HepG2 (ENCLB723FZX)

description:
https://www.encodeproject.org/experiments/ENCSR222QJT/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR222QJT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB723FZX
fragmentation methods: none

tag: line

tag: collection date

tag: link

value: ENCBS868MLR at ENCODE; https://www.encodeproject.org/ENCBS868MLR/


title: MPRA from HepG2 (ENCLB485DHD)

description:
https://www.encodeproject.org/experiments/ENCSR222QJT/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR222QJT
assay title: MPRA
assembly: hg19, GRCh38
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB485DHD
fragmentation methods: none

value: ENCBS236QZU at ENCODE; https://www.encodeproject.org/ENCBS236QZU/


title: MNase-ChIP, Input, Control RNAi, Batch 3

tag: cell type

value: Late-stage Embryonic

value: Control RNAi


title: MNase-ChIP, Input, Control RNAi, Batch 2


title: pooled clone sequencing from DNA cloning sample (ENCLB589SUY)

description:
https://www.encodeproject.org/experiments/ENCSR732JTP/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR732JTP
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB589SUY

value: Ryan Tewhey, JAX

value: not applicable


title: MNase-ChIP, Input, Control RNAi, Batch 1


title: KOAngII628

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

institute: Fujian University of Traditional Chinese Medicine

description: KO mice infused with Ang Ⅱ(500 ng/kg/min)

data_processing:
Utilize the bcl2fastq software to perform Base Calling on the original image files from Illumina high-throughput sequencing and convert them into original sequencing reads.
Use the FastQC software to analyze the base quality from 5' to 3' of the sequencing reads and assess the content of A, T, C, and G bases in the sequencing data, evaluating the base type ratio at each position from an overall level.
Utilize the fastp software to filter the raw data, removing reads that do not meet the analysis criteria, in order to obtain clean reads that can be used for subsequent alignment, statistics, and further analysis.
After quality control of the raw sequencing data, clean data is obtained. The clean data is then assessed to review the effectiveness of the quality control, and ultimately, the clean data is used for analysis.
Read count extraction and normalization were performed using RseQC software
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: abdominal aorta

extract_protocol:
RNA was harvested using TRIzol® Reagent (invitrogen.). 1 µgof total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nebnext ultra-RNA library preparation kit following manufacturer's protocols.

tag: tissue

value: abdominal aorta

tag: genotype

value: AngII


title: KOAngII537


title: KOAngII560


title: pooled clone sequencing from DNA cloning sample (ENCLB820DCU)

description:
https://www.encodeproject.org/experiments/ENCSR721WTZ/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR721WTZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB820DCU
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

value: DNA cloning sample

value: cloning host


title: KOAngII612


title: KOAng_II402


title: MPRA from SK-N-SH (ENCLB540TLG)

description:
https://www.encodeproject.org/experiments/ENCSR087VPA/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR087VPA
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB540TLG
fragmentation methods: none

source_name: Homo sapiens SK-N-SH cell line genetically modified (episome) using transient transfection, 24 hours post-nucleic acid delivery time

value: SK-N-SH

value: cell line

tag: geographic location

tag: encode accession

value: female

tag: health state

value: Metastatic neuroblastoma from bone marrow

value: 4 years

value: ATCC

value: ENCBS234PAV at ENCODE; https://www.encodeproject.org/ENCBS234PAV/


title: Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor IHGF, replicate M2

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
Reads were mapped to the human genome using STAR, v. 2.7.9a.
For genome annotation, the GENCODE GRCh38 annotation, p25 was used. Raw counts were collected using feature counts.
For QC, several packages were used, including FastQC (v. 0.11.9), dupradar, infer-experiment, QualiMap (v. 2.2.2) and MultiQC (v. 1.10.1)
Differential gene expression analysis was performed with the R package DESeq 2, v. 1.30.1. Gene set enrichment analysis was done using the R package tmod, v. 0.50.13.
Assembly: GRCh38 v. p7
Supplementary files format and content: raw_counts.tsv is a tab-separated file containing gene annotation information and raw counts for all samples.

source_name: oral mucosa

growth_protocol: primary gingival fibroblasts were isolated from gingival biopsies and maintained in Dulbecco’s modified Eagle’s medium (DMEM, PAN Biotech, Germany) supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 1% non-essential amino acids (MEM-NEAA, PAN Biotech) and and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from pGF cells using the RNeasy Mini Kit (Qiagen).
500 ng total RNA of transfected cell cultures were used for library generation with the TrueSeq stranded total RNA kit (Illumina). Libraries were sequenced with 16 million reads (75 bp single end) on a NextSeq 500 using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles).

treatment_protocol: Cell cultures of primary gingival fibroblasts from 3 different donors were transfected with LNA GapmeRs targeting the lncRNA CDKN2B-AS1 or negative control GapmeRs and harvested after 48 hours.

value: oral mucosa

value: primary cells

value: gingivial fibroblasts

tag: donor code

value: IHGF

tag: replicate


title: pooled clone sequencing from DNA cloning sample (ENCLB033IGT)

description:
https://www.encodeproject.org/experiments/ENCSR721WTZ/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR721WTZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB033IGT
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

value: synthetic construct

tag: age

value: 60 days

value: Ryan Tewhey, JAX

tag: Sex


title: MPRA from SK-N-SH (ENCLB038ULL)

description:
https://www.encodeproject.org/experiments/ENCSR087VPA/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR087VPA
assay title: MPRA
possible controls: ENCSR271KLC
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB038ULL
fragmentation methods: none

value: not applicable

tag: dev stage

value: child

tag: passage number

tag: source

value: ENCBS577VWL at ENCODE; https://www.encodeproject.org/ENCBS577VWL/


title: pooled clone sequencing from DNA cloning sample (ENCLB866ZVE)

description:
https://www.encodeproject.org/experiments/ENCSR721WTZ/
***************
biological replicate number: 5
technical replicate number: 1
description:
experiment encode accession: ENCSR721WTZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB866ZVE
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

value: DNA cloning sample

value: cloning host

tag: biosample encode accession

tag: biosample term name

tag: lab


title: Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor IHGF, replicate N2

tag: cell line

tag: treatment

value: negative control GapmeRs


title: pooled clone sequencing from DNA cloning sample (ENCLB796BLY)

description:
https://www.encodeproject.org/experiments/ENCSR721WTZ/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR721WTZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB796BLY
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000


title: KONS_608

description: WT mice infused with Saline

tag: tissue

value: abdominal aorta

value: KONS

value: Saline


title: Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor pFB39, replicate M2

tag: cell type


title: pooled clone sequencing from DNA cloning sample (ENCLB785YTT)

description:
https://www.encodeproject.org/experiments/ENCSR721WTZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR721WTZ
assay title: pooled clone sequencing
encode release date: 2023-02-12
lab: Ryan Tewhey, JAX
library encode accession: ENCLB785YTT
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000


title: Explant-5d-P-5

city: London

first: Ferdinand

last: Marlétaz

address: Gower Street

department: Genetics, Evolution & Environment

institute: University College London

description:
5 days post amputation, Proximal segment, Replicate 5
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-P-5

data_processing:
Counts and TPMs were obtained using Kallisto
Supplementary files format and content: normalised read counts

molecule: polyA RNA

organism: Amphiura filiformis

source_name: Regenerating explant

extract_protocol:
RNA-seq: RNA extracted with RNAeasy micro RNA kit
RNA-seq: Strand-specific RNA-seq libraries were prepared using the TruSeq RNA Library (Illumina) and sequenced in a 2x150bp layout.

value: Regenerating explant

tag: time point

value: 5 days post amputation

tag: segment

value: Proximal segment

value: Whole arm

tag: genotype

value: WT

value: No treatment


title: KONS_555

description: WT mice infused with Saline


title: pooled clone sequencing from DNA cloning sample (ENCLB443BHV)

description:
https://www.encodeproject.org/experiments/ENCSR466AMS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR466AMS
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB443BHV
instrument models: Illumina NextSeq 500,Illumina NovaSeq 6000

value: synthetic construct

value: 60 days


title: Explant-5d-P-4

description:
5 days post amputation, Proximal segment, Replicate 4
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-P-4


title: KONS_387

description: WT mice infused with Saline


title: Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor pFB3, replicate M1

value: oral mucosa

value: primary cells

value: gingivial fibroblasts

tag: donor code


title: Homo sapiens oral mucosa gingivial fibroblasts, LNA GapmeRs targeting the lncRNA CDKN2B-AS1, donor pFB2, replicate M2

tag: replicate


title: WTAngII581

description: WT mice infused with Ang Ⅱ(500 ng/kg/min)

value: AngII


title: pooled clone sequencing from DNA cloning sample (ENCLB978ANM)

description:
https://www.encodeproject.org/experiments/ENCSR448FBS/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR448FBS
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB978ANM

value: DNA cloning sample

value: cloning host

tag: age

value: Ryan Tewhey, JAX

value: not applicable


title: Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor pFB3, replicate N1

value: negative control GapmeRs


title: pooled clone sequencing from DNA cloning sample (ENCLB099LVY)

description:
https://www.encodeproject.org/experiments/ENCSR448FBS/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR448FBS
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB099LVY

tag: Sex


title: KONS_627

description: WT mice infused with Saline

value: abdominal aorta

value: KONS

value: Saline


title: Explant-5d-P-1

description:
5 days post amputation, Proximal segment, Replicate 1
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-P-1

value: Regenerating explant

value: 5 days post amputation

value: Proximal segment

value: Whole arm


title: Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor pFB2, replicate N1


title: Explant-5d-M-5

description:
5 days post amputation, Medial segment, Replicate 5
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-M-5

value: Medial segment

value: WT

value: No treatment


title: pooled clone sequencing from DNA cloning sample (ENCLB845YWC)

description:
https://www.encodeproject.org/experiments/ENCSR367WAO/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR367WAO
assay title: pooled clone sequencing
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB845YWC

value: synthetic construct

value: 60 days


title: pooled clone sequencing from DNA cloning sample (ENCLB059GZK)

description:
https://www.encodeproject.org/experiments/ENCSR367WAO/
***************
biological replicate number: 4
technical replicate number: 1
description:
experiment encode accession: ENCSR367WAO
assay title: pooled clone sequencing
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB059GZK

value: DNA cloning sample


title: WTAng_II536

value: AngII


title: Explant-5d-M-1

description:
5 days post amputation, Medial segment, Replicate 1
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-M-1


title: Explant-5d-M-2

description:
5 days post amputation, Medial segment, Replicate 2
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-M-2


title: WTAngII568


title: Homo sapiens oral mucosa gingivial fibroblasts, negative control GapmeRs, donor pFB39, replicate N2

value: oral mucosa

value: primary cells

value: gingivial fibroblasts


title: pooled clone sequencing from DNA cloning sample (ENCLB170TUK)

description:
https://www.encodeproject.org/experiments/ENCSR367WAO/
***************
biological replicate number: 3
technical replicate number: 1
description:
experiment encode accession: ENCSR367WAO
assay title: pooled clone sequencing
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB170TUK

value: cloning host

value: Ryan Tewhey, JAX

value: not applicable


title: Explant-5d-D-5

description:
5 days post amputation, Distal segment, Replicate 5
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-D-5

value: Regenerating explant

value: Distal segment


title: KONS_412

description: WT mice infused with Saline

value: abdominal aorta

value: KONS

value: Saline


title: WTAng_II519


title: ChIP-Seq JDP2KO IRF2BP2 (repl2)

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

institute: Philipps University of Marburg

data_processing:
ChIP-Seq data were aligned to human Genome hg38 using bowtie allowing one mismatch.
Bigwig fiiles were obtained using deepTools/bamCoverage.
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: THP1 cells were grown in RPMI Medium 1640 (1X) + GlutaMAX (gibco 61870-010), supplemented with FBS (10% v/v), penicillin (100 units/mL), and streptomycin (100μg/mL).

extract_protocol:
ChIP experiments were performed in accordance to the One Day ChIP kit protocol (Diagenode).
For ChIP-Seq library five nanograms of precipitated DNA were used for indexed sequencing library preparation using the Microplex library preparation kit v2 (Diagenode).

treatment_protocol: ATF7 KO and JDP2 KO cells were obtained upon transfection with the respective Lenti-CRISPRv2 constructs. Single cell clones were obtained via limited dilution.

value: AML cell line

value: JDP2 KO

tag: chip antibody

value: IRF2BP2, Sigma-Aldrich, HPA027815


title: WTAngII580


title: pooled clone sequencing from DNA cloning sample (ENCLB647ZUH)

description:
https://www.encodeproject.org/experiments/ENCSR367WAO/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR367WAO
assay title: pooled clone sequencing
encode release date: 2021-07-02
lab: Ryan Tewhey, JAX
library encode accession: ENCLB647ZUH

value: synthetic construct

value: 60 days


title: ChIP-Seq JDP2KO ATF7 (repl2)

value: ATF7, Bethyl Laboratories, A302-431A


title: WTNS_550

description: WT mice infused with Saline

value: WTNS


title: ChIP-Seq ATF7KO ATF7 (repl2)

value: ATF7 KO


title: Explant-5d-D-2

description:
5 days post amputation, Distal segment, Replicate 2
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-D-2

value: 5 days post amputation

value: Whole arm

value: WT

value: No treatment


title: pooled clone sequencing from DNA cloning sample (ENCLB777GFJ)

description:
https://www.encodeproject.org/experiments/ENCSR273YHW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR273YHW
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB777GFJ

value: DNA cloning sample

value: cloning host

value: Ryan Tewhey, JAX

value: not applicable


title: Explant-5d-D-1

description:
5 days post amputation, Distal segment, Replicate 1
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
5d-D-1

value: Regenerating explant

value: Distal segment


title: pooled clone sequencing from DNA cloning sample (ENCLB770IYR)

description:
https://www.encodeproject.org/experiments/ENCSR271KLC/
***************
biological replicate number: 2
technical replicate number: 1
description:
experiment encode accession: ENCSR271KLC
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB770IYR


title: WTNS_547

description: WT mice infused with Saline

value: abdominal aorta

value: Saline


title: Explant-3d-P-4

description:
3 days post amputation, Proximal segment, Replicate 4
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-P-4

value: 3 days post amputation

value: Proximal segment


title: WTNS_523

description: WT mice infused with Saline


title: ChIP-Seq WT ATF7 (repl2)

value: AML cell line

value: ATF7, Bethyl Laboratories, A302-431A


title: pooled clone sequencing from DNA cloning sample (ENCLB867DTR)

description:
https://www.encodeproject.org/experiments/ENCSR271KLC/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR271KLC
assay title: pooled clone sequencing
encode release date: 2024-04-25
lab: Ryan Tewhey, JAX
library encode accession: ENCLB867DTR

value: synthetic construct

value: 60 days


title: ChIP-Seq WT IRF2BP2 (repl2)

value: IRF2BP2, Sigma-Aldrich, HPA027815


title: WTNS_373

description: WT mice infused with Saline

value: WTNS


title: L. acidophilus

city: Donostia

first: Alex

middle: Martínez

last: Ascensión

state: Gipuzkoa

address: P/ Doctor Begiristain

country: Spain

institute: Biogipuzkoa HRI

description: ACIDOLA

data_processing:
Reads from samples were mapped to human references twice. A first map was performed using GRCh38 (Ensembl version 109) using nf-core/rnaseq v3.12.0 module, with STAR v2.7.9a as mapper. Unmapped reads were again mapped, this time using bowtie2 v2.4.5 with --very-sensitive argument and CHM13 genome version.
Unmapped reads are then mapped using different profilers: kaiju, kraken2, krakenuniq and centrifuge. For each profiler, specific available databases were downloaded or constructed consisting, at least of human, archaeal, bacterial, viral and fungal genomes. After individual profiling was performed, taxpasta v0.3.0 was used to standardise the outputs of each profiler into a common format. Taxa lineages were cut at the genus level.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file with raw counts per sample

organism: Lactobacillus acidophilus

source_name: Culture

extract_protocol:
The concentration and quality of the RNA pools was measured using Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA) before library preparation at CD Genomics (Shirley, New York, NY, USA). After normalization, rRNA was depleted from the total RNA sample using the Ribo-Zero rRNA removal kit (Illumina, San Diego, CA, USA) and followed by purification and fragmentation steps.
Strand-specific cDNA synthesis was performed, the 3′ ends were adenylated, and adaptors were ligated. The resulting libraries were subjected to standard quality control and normalization processes. Paired-end sequencing was performed with Illumina HiSeq X Ten (Illumina, San Diego, CA, USA), and an average of 40–50 × 10^6 reads were obtained per sample.

value: Culture

value: bacterial cell

tag: disease state

value: Sample control


title: Explant-3d-P-2

description:
3 days post amputation, Proximal segment, Replicate 2
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-P-2

value: Whole arm

value: WT

value: No treatment


title: WTNS_369

description: WT mice infused with Saline


title: Explant-3d-M-4

description:
3 days post amputation, Medial segment, Replicate 4
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-M-4

value: Regenerating explant

value: Medial segment


title: ChIP-Seq JDP2KO IRF2BP2 (repl1)

value: JDP2 KO


title: ChIP-Seq ATF7KO IRF2BP2 (repl1)

value: ATF7 KO


title: Explant-3d-M-3

description:
3 days post amputation, Medial segment, Replicate 3
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-M-3

value: 3 days post amputation


title: Explant-3d-M-1

description:
3 days post amputation, Medial segment, Replicate 1
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-M-1


title: ChIP-Seq WT ATF7 (repl1)

value: AML cell line


title: ChIP-Seq ATF7KO ATF7 (repl1)

value: ATF7, Bethyl Laboratories, A302-431A


title: ChIP-Seq ATF7KO IRF2BP2 (repl2)


title: Explant-3d-P-3

description:
3 days post amputation, Proximal segment, Replicate 3
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-P-3

value: Proximal segment


title: ChIP-Seq WT IgG (repl1)

value: IgG, Diagenode, C15410206


title: ChIP-Seq WT IRF2BP2 (repl1)

value: IRF2BP2, Sigma-Aldrich, HPA027815


title: C_mt of TAp73 biological rep2 batch 2

type: RNA

city: Singapore

first: Kanaga

last: Sabapathy

state: Singapore

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University Singapore

hyb_protocol: Hybridization was performed according to standard protocols.

scan_protocol: Scanning was performed according to standard protocols.

data_processing: The R package affy was used for data processing. The rma function (Robust Multiarray Average) was used for quantile normalization and background correction.

label: biotin

source_name: lung cancer cell line

label_protocol: Labeling was performed according to standard Affymetrix protocols.

growth_protocol: H1299 cells were cultured with DMEM medium with 10% FBS and 1% PenStrep

extract_protocol: Total RNA was extract by using RNA extraction Kit

treatment_protocol: Retrovirus carrying TAp73 was generated by transfecting 293T cells with pBABE empty vector or those with the respective genes, together with the helper plasmids. H1299 cells were infected with harvested retrovirus soup for 48 hrs, and were selected with 2 µg/ml puromycin for another 2 days, and used for the experiments.

tag: transfection

value: C_mt of TAp73


title: Explant-3d-D-3

description:
3 days post amputation, Distal segment, Replicate 3
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-D-3

value: Distal segment


title: C_mt of TAp73 biological rep1 batch 2


title: ChIP-Seq WT IgG


title: ChIP-Seq JDP2KO ATF7 (repl1)


title: Explant-3d-D-4

description:
3 days post amputation, Distal segment, Replicate 4
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-D-4


title: Regeneration time serie Control

description:
Control
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: Control


title: N_mt of TAp73 biological rep1 batch 2

value: N_mt of TAp73


title: Explant-3d-D-1

description:
3 days post amputation, Distal segment, Replicate 1
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-D-1

value: Whole arm


title: Explant-3d-D-2

description:
3 days post amputation, Distal segment, Replicate 2
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-D-2

value: WT


title: T1D_Patient_8_RNA_RNAseq_1

value: plasma


title: Explant-3d-M-2

description:
3 days post amputation, Medial segment, Replicate 2
REGEN-EXPLANTS_tmm_normalized_gene_expression_table.tsv
3d-M-2

value: Regenerating explant

value: No treatment


title: Regeneration time serie 50% D

description:
50% D
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

source_name: Regenerating arm

value: Regenerating arm

value: 50percent D


title: T1D_Patient_7_RNA_RNAseq_1


title: N_mt of TAp73 biological rep2 batch 2


title: WT-TAp73 biological rep2 batch 2


title: Regeneration time serie 50% P

description:
50% P
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: 50percent P


title: WT-TAp73 biological rep1 batch 2


title: T1D_Patient_6_RNA_RNAseq_1


title: Control biological rep1 batch 2

value: control


title: Regeneration time serie Stage 5

description:
Stage 5
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: Stage 5


title: T1D_Patient_5_RNA_RNAseq_1


title: ChIP-Seq WT IRF2BP2

value: AML cell line


title: Regeneration time serie Stage 4

description:
Stage 4
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: Stage 4


title: Control biological rep2 batch 2


title: N_C_mt of TAp73 biological rep3 batch 1

value: N_C_mt of TAp73


title: N_C_mt of TAp73 biological rep1 batch 1


title: T1D_Patient_2_RNA_RNAseq_1


title: T1D_Patient_3_RNA_RNAseq_1


title: Regeneration time serie Stage 3

description:
Stage 3
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: Stage 3


title: N_C_mt of TAp73 biological rep2 batch 1


title: Regeneration time serie 72 hpa

description:
72 hpa
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: 72 hpa


title: WT-TAp73 biological rep3 batch 1


title: T1D_Patient_1_RNA_RNAseq_1


title: B. lactis

description: BLACTIS

organism: Bifidobacterium animalis subsp. lactis

value: Culture

value: bacterial cell

value: Sample control


title: WT-TAp73 biological rep2 batch 1


title: WT-TAp73 biological rep1 batch 1


title: Natural and artificial sequences, 1M7 denaturated sample, without Mg, without SAM, replicate 1

status: Public on May 06 2024

city: Paris

first: Pierre

last: HARDOUIN

state: France

address: 4 avenue de l'observatoire

department: CiTCoM

country: France

institute: Faculté de pharmacie UMR 8038

description:
Multiple bacterial species (RFAM RF00162)
dsDNA library, 206 SAM-I aptamer natural sequences and 100 Artificial sequences

library_source: other

data_processing:
The demultiplexing is made using cutadapt. (https://cutadapt.readthedocs.io/en/stable/)
Quality trimming, Paired read merging, Sequence alignment, Mutation identification, Mutation counting, Sequence correction, reactivity profile calculation were made by using Shapemapper 2 (https://github.com/Weeks-UNC/shapemapper2)
Assembly: N/A
Supplementary files format and content: Tab-separated values files

molecule: other

organism: Bacteria

source_name: bacteria

extract_protocol:
N/A
RNAs were in vitro transcribed, modified with SHAPE reagent and reverse transcribed with the Superscript III reverse transcriptase (Invitrogen®) and NGS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs®) as manufacter’s instructions.

value: bacteria


title: Natural and artificial sequences, Untreated sample, DMSO, replicate 1


title: Natural and artificial sequences, 1M7 treated sample, 5mM Mg, without SAM, replicate 1


title: Natural and artificial sequences, 1M7 treated sample, 5mM Mg, 1mM SAM, replicate 1


title: Natural and artificial sequences, 1M7 treated sample, 5mM Mg, 0,1mM SAM, replicate 1


title: Control biological rep3 batch 1


title: Control biological rep2 batch 1


title: Natural and artificial sequences, 1M7 treated sample, without Mg, without SAM, replicate 1


title: Natural and artificial sequences, 1M7 treated sample, 5mM Mg, 0,1mM SAM, replicate 0


title: Natural and artificial sequences, 1M7 treated sample, 5mM Mg, 1mM SAM, replicate 0


title: Natural and artificial sequences, 1M7 denaturated sample, without Mg, without SAM, replicate 0


title: T1D_Patient_4_RNA_RNAseq_1

value: plasma


title: Control biological rep1 batch 1


title: MNase-ChIP, Input, Set2 (1) 7-day RNAi, Batch 0

value: Late-stage Embryonic

value: Set2 RNAi


title: MNase-ChIP, Input, Control_2 7-day RNAi, Batch 0

value: Control RNAi


title: Natural and artificial sequences, 1M7 treated sample, 5mM Mg, without SAM, replicate 0


title: WT cells biological replicate 3

city: Zurich

first: Marco

last: La Fortezza

state: Zurich

address: Universitätstrasse 16

department: Environmental Systems Science

country: Switzerland

institute: ETH Zurich

data_processing:
FastQC
Timmotatic
bowtie and HTSeq
DESeq2
Assembly: DK1622
Supplementary files format and content: xlsx file containing DESeq results
Supplementary files format and content: tab delimited data, containing raw counts per transcript

organism: Myxococcus xanthus

source_name: bacterial liquid culture

growth_protocol: Liquid culture in CTT, casitone based media. 32 °C at 300 rpm.

extract_protocol:
RNeasy Mini  Kit from Qiagen (ID: 74004)
Total RNA Illumina, prepared at the Functional Genomic Center, UZH.

treatment_protocol: Knock-out mutation, same growth conditions

value: bacterial liquid culture

value: vegetative cells

value: wild-type (GJV1) - derived DK1622

value: WT


title: cells lacking pxr, biological replicate 2

value: delta-pxr (GJV1::d-pxr)

value: delta-pxr


title: cells lacking pxr, biological replicate 1


title: wholeBlood_Hive_30k

city: Melbourne

first: Daniel

middle: Victor

last: Brown

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

description: Reverse transcription based sequencing

data_processing:
Samples were demultiplexed with bcl2fastq v2.20.0. HIVE libraries were preprocessed with Honeycomb BeeNet, v1.1 with genome reference GRCh38.104. 10x Genomics Flex libraries were preprocessed with Cell Ranger multi v7.1.0, the probe set reference was v1.0.1 and human genome reference GRCh38-2020-A.
Assembly: HIVE libraries genome reference was GRCh38.104. 10x Genomics Flex libraries probe set reference was v1.0.1 and human genome reference was GRCh38-2020-A.
Supplementary files format and content: R Data Serialization (.rds) object that can be read into R with the readRDS() function

source_name: Whole blood

extract_protocol:
Blood was collected from healthy volunteers and collected into either NaCit or EDTA collection tubes. RBCs were lysed for 20 mins in 1x ACK Buffer. Cells were washed in PBS twice by centrifugation at room temperature for 5 min at 350g. Fixation was performed according to each scRNA-Seq kit  manufacturer specific protocol. The number of cells fixed is indicated experimental metadata.
Honeycomb HIVE libraries were processed with manufacture’s protocol cat 10347 v.0.3 revA. 10x Genomics Flex batches 1 and 2 were performed with Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples CG000527, Rev B. Batches 3 and 4 were performed with, Rev D. There are no material differences in reagents or workflow with Rev B being a more detailed protocol than B.

value: Whole blood

value: Healthy donor


title: wholeBlood_Hive_15k

description: Reverse transcription based sequencing


title: cells lacking pxr, biological replicate 3


title: Regeneration time serie 48 hpa

description:
48 hpa
REGEN-TIME-COURSE_tmm_normalized_gene_expression_table.tsv

value: Regenerating arm

value: 48 hpa

value: Whole arm

value: No treatment


title: Natural and artificial sequences, 1M7 treated sample, without Mg, without SAM, replicate 0

value: bacteria


title: wholeBlood_Flex_batch4

description: Ligation probe based sequencing


title: WT cells biological replicate 2


title: WT cells biological replicate 1


title: wholeBlood_Flex_batch3A

description: Ligation probe based sequencing


title: wholeBlood_Flex_batch3B

description: Ligation probe based sequencing


title: wholeBlood_Flex_batch1

description: Ligation probe based sequencing


title: Natural and artificial sequences, Untreated sample, DMSO, replicate 0


title: wholeBlood_Flex_batch2

description: Ligation probe based sequencing


title: S1-seq_wt_timecourse_14dpp__rep2

city: New York

first: Soonjoung

last: Kim

email: kims16@mskcc.org, soonjk@yuhs.ac

state: New York

address: 430 East 67th Street

institute: Memorial Sloan Kettering Cancer C

data_processing:
After Qubit quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. We obtained paired-end reads of 50 bp. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes. Base calls were perfomed using bcl2fastq software v.2.20 or bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500, NextSeq 2000, or HiSeq 4000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>. Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000.  (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).
Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.
Reads for S1, Exo7/T, or ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Maps were analyzed using R version 4.0.3 <http://www.r-project.org>.
Assembly: mm10
Supplementary files format and content: BigWig files contain read counts at positions of resection endpoints. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.

source_name: testis

extract_protocol:
Testis cells from mice at indicated age were obtained as described previously (ref. 1). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing, and DNA was liberated by treatment with SDS and proteinase K as described previously (ref. 1).  (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020).
In-plug overhang removal with S1 endonuclease for S1-seq, exonuclease VII and exonuclease T for Exo7/T-seq, or exonuclease T for ExoT-seq, and adaptor ligation were performed as described previously (ref. 1, 2, 3) with minor modifications. In brief for S1-seq, plugs were washed in 0.5 ml of modified S1 buffer (50 mM sodium acetate, 280 mM NaCl, 4.5 mM ZnSO4, pH 4.7) for 30 min four times, treated with 9 units of S1 nulcease in 500 µl of modified S1 buffer at 37°C for 20 min and washed once with 1ml TE. For Exo7/T-seq, plugs were washed in 1 ml of exonuclease VII buffer for 15 min twice, treated with 50 units of exonuclease VII in 100 µl of exonuclease VII buffer at 37°C for 60 min and washed once with 1ml TE and followed by exonulcease T treamtment. For ExoT-seq, plugs were washed in 1 ml of NEBuffer 4 for 15 min 3 times, treated with 75 units of exonuclease T in 100 µl of NEBuffer 4 at 24°C for 90 min and washed 3 times with 8 ml of TE for 15 min. The nuclease treated ssDNA ends were further polished with T4 polymerase before the first adaptor ligation as previously described (ref. 1, 2, 3). After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously (ref. 1, 2, 3).  (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020).  (ref. 2) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017).  (ref. 3) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
S1-seq, Exo7/T-seq, ExoT-seq

value: testis

tag: strain

value: Spermatocytes

value: wild type

value: 14 days post partum


title: E7T-seq_CtIPcKO_5wo

value: CtIP-cKO

value: 5 weeks old


title: S1-seq_Exo1DA_16dpp_rep2

value: 16 days post partum


title: S1-seq_CtIPcKO_14dpp


title: S1-seq_wt_timecourse_12dpp_rep2

value: 12 days post partum


title: S1-seq_Nbs1dB_16dpp_rep1


title: S1-seq_wt_timecourse_16dpp__rep2


title: S1-seq_wt_timecourse_13dpp_rep2

value: 13 days post partum


title: S1-seq_Nbs1dB_Exo1DA_16dpp_rep2

value: Nbs1{delta}B Exo1DA


title: S1-seq_Nbs1dBhet_14dpp_rep2

value: Nbs1{delta}B het


title: S1-seq_Rad50DY_14dpp_rep2


title: S1-seq_Nbs1dB_16dpp_rep2


title: E7T-seq_Mre11HNhet_5wo

value: Mre11-HN het


title: S1-seq_Mre11cHN_14dpp


title: S1-seq_Mre11cKO_5wo_rep2


title: S1-seq_Rad50LF_14dpp_rep2


title: E7T-seq_Mre11cHN_5wo_rep1


title: E7T-seq_Mre11cHN_5wo_rep2


title: S1-seq_Mre11cKO_5wo_rep1


title: S1-seq_Mre11cKO_14dpp


title: E7T-seq_Mre11cKO_5wo_rep2


title: S1-seq_wt_timecourse_15dpp__rep2

value: 15 days post partum


title: Microglia 3 ATAC-seq

city: Tampa

first: jiqiang

last: yao

address: 12902 USF Magnolia Drive

institute: moffitt cancer center

description: BMDMMinusMG.narrowpeaks.DE.txt

data_processing:
Read adapters were detected using BBMerge (v37.02) and subsequently removed with cutadapt (v1.8.1).
Processed raw reads were then aligned to mouse genome mm10 using BOWTIE2 (v2.4.1).
Peak Calling was performed performed to identify regions of open chromatin  using MACS2 (v 2.1.1.20160309).
Only peaks significantly enriched than background with q <0.01 were considered confident and subjected for downstream analysis.
Peaks were annotated by ChIPseeker (v1.32.1) [5] with gene model TxDb.Mmusculus.UCSC.mm10.knownGene (v 3.10.0).
Consensus peak identifiers were obtained by GenomicRanges (v1.48.0).
Peaks were then normalized and differential analysis between experimental groups were evaluated using DEseq2 (v1.36.0).
Assembly: mm10
Supplementary files format and content: text;differential comparison
Supplementary files format and content: text;narrowpeak

source_name: brain tumors

growth_protocol: MG(F4/80+CD11b+CD45loLY6Clo/-LY6G-CD49dlo/-) and BMDM (F4/80+CD11b+CD45+LY6Clo/-LY6G-CD49dhigh) were FACS-sorted from brain tumors

extract_protocol:
The ATAC-seq protocol was done mostly as described previously. Briefly, 5 x 104 cells were washed in 50μl cold PBS, spun down at 500 x g and 4°C for 5 mins, and resuspended in 50μl cold lysis buffer.Resuspended cells were immediately spun at 500 x g and 4°C for 10mins, and the supernatant was remvoed.
DNA was extracted using Nextera Tn5 transposase kit. PCR amplification of tagmented DNA was done using the NEBNext 2X mastermix.

treatment_protocol: Brain tumors (SB28) established orthotopically in the mouse brain

value: brain tumors

value: WT

value: FACS-sorted from isogenic SB28 brain tumors established orthotopically in the mouse brain


title: Bone marrow derived macrophages 1 ATAC-seq

description: BMDMMinusMG.narrowpeaks.DE.txt


title: Microglia 2 ATAC-seq

description: BMDMMinusMG.narrowpeaks.DE.txt


title: Microglia 1 ATAC-seq

description: BMDMMinusMG.narrowpeaks.DE.txt


title: Williams 82 noninfected RNA bio rep 1 [PG2C_1]

city: Knoxville

first: Tarek

last: Hewezi

state: TN

address: 2431 Joe Johnson Drive

department: Plant Sciences

institute: University of Tennessee

data_processing:
Trimmomatic - fastq trimming and pairing
STAR - mapping the reads to a reference genome
Htseq - counting the reads mapped
DEseq2 - the differential expression analysis
Assembly: Gmax_508_v4.0
Supplementary files format and content: read counts

organism: Glycine max

source_name: Root

extract_protocol:
Hot Phenol RNA extraction from soybean root tissue
mRNA library preperation (polyA enrichment) - NoaSeq PE150 (12G raw data per sample)

value: Root

value: Williams 82 soybean

value: noninfected


title: Williams 82 noninfected RNA bio rep 3 [PG2C_3]


title: KD-GmMKK2 noninfected RNA bio rep 1 [K102C_1]

value: KD-GmMKK2 overexpression


title: Williams 82 H. glycines infected RNA bio rep 2 [PG2R3_2]

value: Heterodera glycines


title: KD-GmMKK2 noninfected RNA bio rep 3 [K102C_3]


title: Williams 82 H. glycines infected RNA bio rep 1 [PG2R3_1]


title: KD-GmMKK2 noninfected RNA bio rep 2 [K102C_2]


title: KD-GmMKK2 H. glycines infected RNA bio rep 1 [K102R3_1]


title: KD-GmMKK2 H. glycines infected RNA bio rep 2 [K102R3_2]


title: KD-GmMKK2 H. glycines infected RNA bio rep 3 [K102R3_3]


title: WT-GmMKK2 noninfected RNA bio rep 3 [W102C_3]

value: WT-GmMKK2 overexpression


title: WT-GmMKK2 H. glycines infected RNA bio rep 3 [W102R3_3]


title: Bone marrow derived macrophages 3 ATAC-seq

description: BMDMMinusMG.narrowpeaks.DE.txt


title: WT-GmMKK2 noninfected RNA bio rep 1 [W102C_1]


title: WT-GmMKK2 noninfected RNA bio rep 2 [W102C_2]


title: Bone marrow derived macrophages 2 ATAC-seq

description: BMDMMinusMG.narrowpeaks.DE.txt


title: IgG_YFP

city: Charlottesville

first: Gary

middle: K

last: Owens

state: VA

address: 415 Lane Road MR5 Building Room 1322

institute: University of Virginia

data_processing:
Basecalls performed using CASAVA
Reads were aligned against mouse genome mm10 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R using Seurat v3. Cells were filtered for 200-5000 reads per UMI, 10% or less mitochondrial and less than 5% hemoglobin gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test with 10000 repetitions, and clusters were calculated as described in the manuscript
Differential expression analysis was done using MAST
Assembly: mm10
Supplementary files format and content: Cell-gene-barcode matrices

source_name: Atherosclerosis plaques

extract_protocol:
Individual atherosclerotic plaques from the brachiocephalic artery were removed from underlying media with forceps and deposited into FACS buffer (1% BSA in PBS) plus 1 ug/mL Actinomycin D,(Gibco, #11805017). Samples were then minced and digested with 1mL Liberase (Roche, #355374) plus 1ug/mL ActinomycinD for 1 hour at 37 degrees, then resuspended in PBS plus 0.04% UltraPure non-Acetylated BSA (ThermoFisher #AM2616) and filtered through 30um filters on ice. Samples were then either counted and submitted directly for scRNAseq or sorted by flow cytometry. Samples for flow were stained with Sytox Blue viability dye and sorted with a BD FACSAria Fusion cell sorter with gating on live, single cells that were eYFP+. Cells were collected into LoBind tubes containing 0.04% non-acetylated BSA.
2,000 cells in each group were targeted in Chromium 10X genomics libraries, which after barcoding, were pooled and sequenced on the Illumina NextSeqTM, 150 cycle high-output.
single-cell RNA-seq (10x genomics, 3')

treatment_protocol: Animals were maintened in a Western Diet for 18 weeks

value: Atherosclerosis plaques

value: Sorted eYFP+ SMC cells

value: Apoe-/-


title: IgG_Live

value: Mixture of cell types (SMC, Epithelial, Macrophage, others)


title: IgG_CD45

value: CD45 Sorted cells


title: Ab_CD31

value: CD31 Sorted cells


title: Ab_YFP


title: Williams 82 noninfected RNA bio rep 2 [PG2C_2]


title: Ab_CD45


title: Ab_Live


title: Williams 82 H. glycines infected RNA bio rep 3 [PG2R3_3]